Ok, by trial-and-error I figured out the answer to question 3. One right-clicks and hold while dragging the mouse up/down to change the radius. I would much prefer to be able to set the contour-level by right clicking-and-hold and drag, since that is something one needs to change much more frequenly than the Zone radius. Also, I realize that Zone does not hide atoms outside of the sphere, so one has to hide atoms first and then zone will show the atoms inside of the sphere.

From: Daniel Larsson via ChimeraX-users <chimerax-users@cgl.ucsf.edu>
Reply to: Daniel Larsson <daniel.larsson@icm.uu.se>
Date: Tuesday, 27 February 2024 at 09:42
To: "chimerax-users@cgl.ucsf.edu" <chimerax-users@cgl.ucsf.edu>
Subject: [chimerax-users] right-mouse clipping

Hi all,

I have some question and comments regarding the very useful right-mouse Clipping tools. I feel they are poorly documented (or documentation is very difficult to find by Google searching).

For the Clip tool, it took me forever to realize how to “undo” the clipping (click again). The Zone clipping is a very nice feature, which shows atoms, residue labels and volume inside of an approximately 10 Å sphere and hides the volume and only show cartoon outside of the sphere. Right-clicking on the background hides the labels.

Some questions

1. How do I change the back/far clipping plane using the Clip tool (the icon suggests that you can clip into a slab)?
2. If so, is it possible to set a default thickness of that slab?
3. Is it possible to change the radius of the Zone clipping tool?
4. Is it possible to disable the cartoon outside of the sphere of the Zone clipping tool?
5. Alternatively have the ability to have an extra front clipping plane, which “intelligently” follows the camera when zooming in (hiding things closer to the centered region when zoomed in more)?
6. I use the mouse mode to center the view and camera pivot point (mousemode middleMode "center or translate"). It is possible to make the Zone clipping tool also center the view + pivot point so that I don’t have to also middle-click every time?

Regards,

Daniel

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